Spark plugs could definitely be fouled. We usually put 6 plugs in with new injectors under warranty.
If your positive the vehicle took the correct injector calibrations I'd start there first. You could still have a clogged cat, but usually the misfires will only be on the one bank with the previously failed fuel injectors. Make sure you don't have any rattling coming from your secondary cat. You can also measure the heat of the primary cats while the vehicle is running, they should be much hotter than the rest of the exhaust. If they aren't its likely the catalyst has broken apart.
BMW master tech
2010 E92 335i 6-speed 25k miles. - For sale.
1989 E30 325i coupe 5-speed DD